XR_007058683.1:n.3604C>G

Variant names:

• chr5-7908246-C-G
• rs327588
• XR_007058683.1:n.3604C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058683.1(LOC124900936):​n.3604C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,046 control chromosomes in the GnomAD database, including 51,287 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51287 hom., cov: 32)
• Consequence: LOC124900936 XR_007058683.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 12 publications found

Genes affected

LOC124900936 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124087 AN: 151928 Hom.: 51236 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.804

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.817 AC: 124208 AN: 152046 Hom.: 51287 Cov.: 32 AF XY: 0.813 AC XY: 60441 AN XY: 74298

African (AFR) AF: 0.886 AC: 36791 AN: 41506

American (AMR) AF: 0.778 AC: 11877 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2539 AN: 5162

South Asian (SAS) AF: 0.834 AC: 4012 AN: 4812

European-Finnish (FIN) AF: 0.772 AC: 8152 AN: 10560

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55359 AN: 67954

Other (OTH) AF: 0.803 AC: 1695 AN: 2110

Alfa AF: 0.732 Hom.: 2147

Bravo AF: 0.817

Asia WGS AF: 0.661 AC: 2299 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.37
PhyloP100		-1.7

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs327588; hg19: chr5-7908359;